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Do Probiotics Cause Bloating, or Could it Be Something Else?

Teasing Out the Real Reason You’re Bloated on Probiotics and What to Do About It

Key Takeaways:

  • Probiotics have few, if any, side effects for most people, but you might avoid potential bloating by choosing a high-quality product without certain ingredients or additives.
  • If you have a particularly sensitive digestive system, trying a high-quality probiotic, one category at a time, may help prevent side effects, including bloating.
  • Probiotic foods are more likely to cause bloating than probiotic supplements due to their high quantity of histamines and other irritants.
  • Persistent bloating seems like a side effect of probiotics if you have unresolved issues like food intolerances, IBS, SIBO, stress, or faulty pelvic or abdominal muscles.
  • You can add science-backed diet changes, supplements, or other treatments to give your probiotics the best chance of relieving your bloating and other symptoms.

Have you noticed an increase in gas, bloating, cramping, or other gastrointestinal symptoms that started around the time you began adding probiotics to your daily routine? While probiotic supplements have a strong safety record (even at very high doses), you may be wondering if they’re to blame for your new symptoms.

It’s not entirely uncommon for people trying a new probiotic to have new symptoms like bloating. Usually, that’s just a sign that you’re adjusting to the changing gut bacteria, and it goes away in less than a week. But for some people, it doesn’t work out so smoothly. In our clinic, probiotics are central to treating patients with an array of symptoms, which means I’ve had a lot of experience helping people troubleshoot their probiotic regimens. 

So, why do some people get bloated after starting probiotics? In general, some probiotics are derived from common allergens, like dairy and egg, which could be responsible for your bloating. Also, many probiotic formulas contain prebiotics, which could be irritating to your system, especially if you have small intestinal bacterial overgrowth (SIBO).

To ensure that you’re maximizing the health benefits of probiotics and minimizing potential side effects, you’ll want to pay attention to the ingredients. Just as important is to make sure you’re buying a good-quality product from a reputable supplement company.

Now let’s look more closely at why you might be bloated after starting a new probiotic regimen. I’ll also guide you on how to avoid bloating, whether or not your probiotic is to blame, and the best ways to safely and smoothly incorporate probiotics into your diet.

Probiotic Bacteria Are Not Likely to Cause Bloating

Though this might seem counterintuitive, it’s highly unlikely that the healthy bacteria in a probiotic formula are to blame for your bloating or other digestive issues [1, 2]. In fact, a large body of quality research has found that probiotics actually relieve bloating better than placebos do, especially for people with irritable bowel syndrome (IBS) [3, 4, 5, 6, 7, 8, 9, 10]. That said, some people are very sensitive to probiotics and may have temporary discomfort as they adjust to them. And sometimes probiotic supplements contain more than just bacteria.

Probiotics are generally considered safe, but like any dietary supplement, quality assurance and the particular ingredients matter. If you experience flatulence, constipation, or changes in bowel movements when introducing a new probiotic formula, it’s possible that the one you’ve chosen isn’t right for you. There are a few ways I’d recommend proceeding if this is the case.

First, Check for Allergens

To make probiotics, manufacturers first create a substrate that provides the nourishment probiotic bacteria (and sometimes fungi) need to grow. Then, they add probiotic strains and wait for them to ferment and multiply. Once they have the desired number of colony-forming units (CFUs), they separate out the probiotic bacteria, use various methods to make them shelf-stable, blend them with other strains if needed, and bottle them up.

Sometimes the initial substrate contains potential irritants like egg or dairy. If you have an allergy or sensitivity to eggs or dairy, then you will want to make sure your probiotic formula is completely egg- and dairy-free [1, 2]. Most probiotics will also highlight that they’re gluten-free, but that’s pretty standard—I’ve never seen a probiotic formula that contains gluten.

Additionally, some supplement companies include excipients, such as fillers, preservatives, or colorants. Excipients should be inert, but some people may react to certain kinds. Some probiotics, especially gummies, also contain flavorings, so be aware of flavoring ingredients when choosing your formula. In general, make sure your product says it’s allergen-free.

Second, Look for Prebiotic Dose

Prebiotics are fibers often included in probiotic formulas that are technically called synbiotics, with the prefix “syn” meaning together. Many healthy foods you regularly eat contain prebiotic fibers, but some people have a hard time digesting them. You might be hard-pressed to find a formula that contains zero prebiotics, so shoot for one that has no more than 3–5 grams per daily serving [11, 12, 13]. 

Third, Ensure Good Quality

Admittedly, it’s hard to know who to trust when it comes to supplements because they aren’t regulated by the Food and Drug Administration (FDA). However, the most reputable supplement companies will have a GMP (Good Manufacturing Practice) stamp indicating their products are consistently of high quality. They will also engage in third-party testing to ensure unbiased quality control. 

When shopping for a probiotic, look for a GMP stamp and a seal from one of the following:

  • National Sanitation Foundation (NSF)
  • The US Pharmacopeia (USP)
  • Consumer Labs (CL)

You can also subscribe to to find out which products they list as safe.

Fourth, Eliminate All But One

If you’re taking multiple categories of probiotics like I recommend in my triple-therapy approach, it’s possible that one of them doesn’t agree with you yet. Taking out two categories to see how you do with one at a time doesn’t have a lot of research behind it. However, the principles of elimination diets and my clinical experience support the idea of trying to isolate what is creating the side effects you’re experiencing. The idea is to start slowly with a low dose of one category and slowly add the others, one by one, to let your body acclimate.There are three categories of probiotics. Category 1 consists of a blend of Lactobacillus and Bifidobacterium species. Category 2 is a healthy yeast called Saccharomyces boulardii, and category 3 is a soil-based probiotic containing various species of Bacillus.

Probiotics causing bloating

Start off with half a recommended dose of Category 1, the most widely available type of probiotic. Using your symptoms as your guide, slowly work your way up to the full dose (10 billion CFU) and stay on that for 2–3 months. However, if you’ve chosen a high-quality, allergen-free, low-prebiotic formula and still have symptoms like bloating after 1 month, your body may not be able to handle one or both of those strains of bacteria right now. 

If bloating persists, discontinue your Category 1 probiotic and move on to a half dose of a different probiotic, one from Category 2. Again, work your way up and stay on the recommended dose (10–15 billion CFU) for 2–3 months. If you still have bloating or other GI symptoms, discontinue and do the same with Category 3 until you reach 2–6 billion CFU.

Probiotics causing bloating

In my many years of experience, I’ve never had a patient who couldn’t tolerate at least one category. Ultimately, as you continue on your gut health journey and begin to heal, you may find that you can reintroduce one or both of the other categories with no side effects.

Die-Off Symptoms

It’s unlikely that die-off reactions would include bloating, but I want to mention them here just in case you experience some of the more common die-off symptoms. 

Also called a Herxheimer reaction, a die-off reaction occurs when you take something (like antibiotics, herbal antimicrobials, or even probiotics) that kills lots of bacteria in your gut. When the bacteria die, they release toxins into your bloodstream, which can set off your immune system. This creates symptoms as your body works to protect you from and get rid of the toxins [1, 2].

When assessing your own symptoms, it’s important to differentiate between temporary and long-term discomfort. Die-off symptoms typically include flu-like fatigue, headache, and brain fog, but none of them should last more than a week. If they do last longer, you’re probably dealing with something complex enough to bring to your healthcare provider. 

Probiotic Foods May Cause Bloating

Interestingly, while it’s unlikely that a probiotic supplement will cause bloating, it’s very possible that probiotic foods, like sauerkraut, kimchi, kombucha, or kefir, could. Bloating is typically associated with probiotic foods rather than probiotic supplements because these foods contain a few potential irritants, such as histamines, FODMAPs, and lactose [14, 15, 16, 17].

Histamines in Fermented Foods

Histamines are a byproduct of the fermentation process that turns fresh foods and juices into probiotic foods. In other words, there are more histamines in fermented foods than in other types of food.

Some people find extra histamines irritating, and some even have histamine intolerance. Histamine intolerance is when the digestive enzymes your body uses to break down histamine in foods aren’t working properly. As a result, histamine can build up and cause symptoms like bloating, nausea, rash, headache, and itching [18].

Since probiotics are made through a process of fermentation, it’s logical to think they contain histamines and could lead to reactions in sensitive people. It’s true that some probiotic strains do produce histamine, but these are not common in probiotic formulas, and we don’t yet know whether probiotics contain enough histamine to incite a reaction. 

Paradoxically, although we need human studies to conclude with any certainty, taking certain probiotic strains could theoretically help improve histamine intolerance [19]. In other words, continually using probiotic supplements may eventually allow you to tolerate fermented foods again in the future, after your digestive system has reset. This may be especially true if you follow a low-histamine diet, which I’ll explain soon.

FODMAPs in Fermented Foods

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, which are short-chain carbohydrates. The small intestine sometimes has a hard time digesting these types of sugars, leading to gas and bloating. This is especially problematic in people with SIBO, whose excessive bacteria in the small intestine make a lot of gas from FODMAPs. 

The most common high-FODMAP probiotic foods are coconut yogurt, dairy yogurt, sauerkraut, and kombucha. These foods (and drinks) contain indigestible carbohydrates that can lead to flatulence and bloating in some people. 

In particular, if you’re dealing with IBS or SIBO, you’ll want to stay away from high-FODMAP foods and lean into a low-FODMAP diet, which I’ll explain more in the next section. Not only will you give yourself a break from gas and bloating, you’ll also begin to kill off the excessive gut bacteria colonizing your small intestine, where they don’t belong.

Lactose in Fermented Foods

I mentioned dairy earlier in the context of supplements, but it’s worth repeating here as well. Dairy-based probiotic foods like yogurt and kefir may cause bloating if you have lactose intolerance.

How to Improve Persistent Bloating

Most likely, you’re taking probiotics to improve some sort of microbial imbalance in your gut that’s causing symptoms. You should expect it to take at least 1–2 months for your gut microbiome to shift and improve on probiotics. But if you continue to experience bloating after 1–2 months, you may need to give your probiotics a helping hand. 

For example, probiotics alone may not be able to fully take care of your bloating if you also have unresolved food intolerances [20, 21, 22, 23], IBS or SIBO [24, 25], stress [26, 27, 28, 29], or dysfunctional abdominal [30] or pelvic floor [31, 32, 33] muscles. The good news is that multiple treatments combined with probiotics can take a firm stand against bloating.

Diets for Bloating Related to Food Intolerances, IBS, or SIBO

  • Low-FODMAP Diet [34, 35, 36, 37, 38, 39] – This diet restricts certain carbohydrates, including those in foods like garlic, onions, stone fruits, and most cruciferous veggies (like broccoli and cabbage) that would otherwise fall into the “healthy food” category. Temporarily avoiding these foods will give your digestive system a break and begin starving out any excessive bacteria in your small intestine that may be the source of your bloating. Even if you don’t have an overgrowth of bacteria in your small intestine, you may have IBS that responds well to removing FODMAPs for a while. Start with this diet and move on to a low-histamine diet if the needle on your bloating doesn’t move.
  • Low-histamine diet [21] – If the low-FODMAP diet doesn’t cut it and you suspect you’re sensitive to high-histamine foods, such as aged cheeses, cured meats, chocolate, and fermented foods, try going low-histamine for about three weeks. If you notice less bloating and other symptoms, such as sniffling, sneezing, headaches, rashes, diarrhea, abdominal pain, or itching, you may have discovered a histamine intolerance. On the bright side, supporting your gut with probiotics could help you tolerate higher-histamine foods over time. But if neither the low-FODMAP nor low-histamine diet is quite enough for your bloating, you can try combining them. 

Whichever dietary route you take, make sure to start reintroducing foods as you feel better to get a full spectrum of nutrients and continually support your improving gut microbiome [40].

Here are some dietary add-ons that may amplify your relief from bloating:

  • Elemental Diet [41] – This may be used as a short-term temporary gut reset alongside any of these plans to help heal underlying issues (like SIBO) contributing to bloating.
  • Low-gluten diet [42] – A low-FODMAP diet is typically low in wheat and therefore gluten, but, when you’re on a low-histamine diet, eating less gluten may reduce bloating even more.
  • Intermittent Fasting [43] – Eating during an 8-hour window and giving your gut a rest for the other 16 hours a day (including the hours you’re sleeping) can accentuate reductions in bloating.
  • Reducing dietary fiber [44] – Fiber triggers bloating in some people. A low-FODMAP diet is typically low in fiber, but reducing your fiber may be a good addition to a low-histamine diet.

Supplements, Medications, and Herbs for Bloating Related to Sluggish Digestion, IBS, or SIBO

  • Digestive enzymes [45, 46, 47, 48] Various enzymes may boost your digestive juices if they’re low, and potentially reduce bloating.
  • Peppermint oil [49, 50, 51, 52, 53, 54) – Peppermint can improve digestion in some people and may reduce bloating. But be careful: Peppermint can make reflux and heartburn worse [55].
  • Antibiotics like rifaximin [49, 56, 57, 58, 59) – This prescription medication can help probiotics eliminate SIBO that may contribute to your bloating.
  • Herbal antimicrobials like Iranian thyme [60] – These can help probiotics eliminate SIBO or other imbalances in gut microbes that could contribute to bloating. 

Stress-Reduction Techniques for Bloating

  • Gut-directed hypnotherapy [61, 62, 63, 64, 65] – With the help of a trained therapist, this can effectively reduce IBS symptoms, including bloating.
  • Cognitive-behavioral therapy [61, 62, 63, 66, 67] – A trained CBT therapist can help you get relief from IBS symptoms like bloating.
  • Meditation [68, 69, 70, 71, 72, 73] – Meditation practices like mindfulness-based stress reduction can calm stress and related bloating.
  • Yoga [74] – Yoga may be good for reducing IBS symptoms such as bloating.
  • Walking [75] – Walking after meals may be a good way to reduce stress and put a dent in abdominal bloating.

Biofeedback Options for Bloating Related to Muscular Dysfunction of the Abdomen or Pelvis 

  • Abdominal biofeedback [69, 76, 77] – You’ll need a skilled practitioner to get started, but breathing-focused biofeedback can reduce bloating.
  • Pelvic floor biofeedback [32, 78] – With help, learning to reduce the effort you put into pooping can help relieve bloating. 

To simplify this long list of action items to help with persistent bloating, I recommend that, with a clinician’s support, you start by adding to your probiotics a low-FODMAP diet and 10–15 minute walks after meals. The low-FODMAP diet can improve symptoms like bloating by reducing inflammation and starving out bad bacteria living in your small intestine [79]. And walking is a no-cost, no-equipment intervention that can improve bloating, belching, flatulence, feelings of over-fullness, and abdominal discomfort [75].

Start there and see how you feel. Keep track of changes in your bloating and other digestive symptoms, and see what has changed after several weeks. The other science-based options are available for you to try if you need a boost, and make sure to check out anything new you try with your healthcare provider.

You Can Navigate Bloating While Taking Probiotics

The relationship between probiotics and bloating is nuanced. While probiotics offer a myriad of potential benefits for the gut microbiome, some people experience digestive symptoms, like bloating, while taking them.

Potential reasons for a digestive reaction may reside inside the bottle of probiotics or within your digestive tract. To deal with potential probiotic product issues, make sure to avoid untested formulas with common allergens like dairy or egg, unnecessary fillers, flavors, or colorants, and more than 3–5 grams of prebiotics.

To address issues with your digestive system, you might add a low-FODMAP diet and short walks after meals, and experiment with other gut-supportive treatments if necessary.

Understanding the factors that may contribute to your bloating and implementing practical strategies can empower you to troubleshoot and improve your digestive health over time. And if you’re looking for extra guidance and support, we’re here to help. Feel free to reach out to our clinic to set up a consultation to get started.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

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